Learn R Programming
⚠️There's a newer version (1.18.5) of this package.Take me there.

VariantAnnotation (version 1.12.9)

Annotation of Genetic Variants

Description

Annotate variants, compute amino acid coding changes, predict coding outcomes

Copy Link

Version

Version

1.12.9

License

Artistic-2.0

Maintainer

Valerie Obenchain

Last Published

February 15th, 2017

Functions in VariantAnnotation (1.12.9)

VariantAnnotation-defunct

Defunct Functions in Package VariantAnnotation
genotypeToSnpMatrix

Convert genotype calls from a VCF file to a SnpMatrix object
getTranscriptSeqs

Get transcript sequences
isSNV

Identification of genomic variant types.
GLtoGP

Convert genotype likelihoods to genotype probabilities
PolyPhenDbColumns

PolyPhenDb Columns
predictCoding

Predict amino acid coding changes for variants
locateVariants

Locate variants
PolyPhenDb-class

PolyPhenDb objects
filterVcf

Filter VCF files
probabilityToSnpMatrix

Convert posterior genotype probability to a SnpMatrix object
PROVEANDb-class

PROVEANDb objects
snpSummary

Counts and distribution statistics for SNPs in a VCF object
summarizeVariants

Summarize variants by sample
ScanVcfParam-class

Parameters for scanning VCF files
SIFTDb-class

SIFTDb objects
scanVcf

Import VCF files
SIFTDbColumns

SIFTDb Columns
readVcf

Read VCF files
refLocsToLocalLocs

refLocsToLocalLocs
VRangesList-class

VRangesList objects
writeVcf

Write VCF files
VariantType-class

VariantType subclasses
VCF-class

VCF class objects
VCFHeader-class

VCFHeader instances
VRanges-class

VRanges objects